NO_JIRA Updated and moved some conformer analysis scripts from confid…

scripts/ReadMe.md

@@ -11,6 +11,10 @@ This folder contains scripts submitted by users or CCDC scientists for anyone to
 
 - A short script to generate conformers with some rudimentary analysis for a single molecule.
 
+## Conformer Filter Density
+
+- A script to filter conformers based on a variety of torsion metrics.
+
 ## Create CASTEP Input
 
 - Creates input files (`.cell` and `.param`) files for a given compound through Mercury.
@@ -19,6 +23,10 @@ This folder contains scripts submitted by users or CCDC scientists for anyone to
 
 - Create GAUSSIAN input file (`.gjf`) for a given CSD refcode or `.mol2` file.
 
+## Filter poses
+
+- A script to filter docking poses based on torsion statistics
+
 ## Find Binding Conformation
 
 - Generates idealized conformers for ligands and evaluates their RMSD to the conformation in the PDB.

scripts/conformer_filter_density/ReadMe.md

@@ -0,0 +1,36 @@
+# Conformer Filter Density
+
+Filter conformers using a variety of metrics described below.
+
+A csv file will be produced with various points of analysis for unusual torsions. Optionally, files containing the
+ conformers which pass and fail within the limits can be written to files.
+
+CCDC Python API Licence required, minimum version: 3.0.15
+
+Script can be run with any multimolecule file e.g. sdf. 
+
+## Instructions on Running
+
+positional arguments: input molecule file
+
+Input file (single- or multi-molecule file)
+
+options:
+* -h, --help; Show this help message and exit
+* -m {absolute,relative}, --mode; Limit mode: absolute (fixed threshold) or relative (threshold based on 
+molecule with fewest unusual torsions). WARNING: Relative mode may behave unexpectedly with conformers from 
+multiple input molecules (default: absolute)
+* -l, --limit; Maximum number of unusual torsions for a passing molecule (default: 0)
+* -d, --local-density; Local density threshold for classifying a torsion as unusual (default: 10.0)
+* --incl-organometallics; Include organometallic compounds in the search (default: organic compounds only)
+* --generalisation; Turn on generalisation for searches
+* --successfn; Output file for molecules that pass the filter (default: successes.mol)
+* --failurefn; Output file for molecules that fail the filter (default: failures.mol)
+* -u, --unusual-torsions; Output CSV file for unusual torsion details (default: unusual_torsions.csv)
+
+
+Originally created by Paul Sanschagrin
+Updated by Chris Ringrose
+
+    For feedback or to report any issues please contact support@ccdc.cam.ac.uk
+

scripts/conformer_filter_density/conformer_filter_density.py

@@ -0,0 +1,189 @@
+#!/usr/bin/env python3
+#
+# This script can be used for any purpose without limitation subject to the
+# conditions at https://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx
+#
+# This permission notice and the following statement of attribution must be
+# included in all copies or substantial portions of this script.
+#
+# 2026-02-03: created by the Cambridge Crystallographic Data Centre
+
+import argparse
+import csv
+
+from ccdc import conformer, io
+
+
+def parse_args():
+    """Parse command line arguments."""
+    parser = argparse.ArgumentParser(description=__doc__)
+
+    parser.add_argument('inmolfn',
+                        metavar='<input molecule file>',
+                        help='Input file (single- or multi-molecule file)')
+
+    parser.add_argument('-m', '--mode',
+                        choices=['absolute', 'relative'],
+                        default='absolute',
+                        help='Limit mode: absolute (fixed threshold) or relative '
+                             '(threshold based on molecule with fewest unusual torsions). '
+                             'WARNING: Relative mode may behave unexpectedly with conformers '
+                             'from multiple input molecules (default: %(default)s)')
+
+    parser.add_argument('-l', '--limit',
+                        dest='torsion_limit',
+                        type=int,
+                        default=0,
+                        metavar='<limit>',
+                        help='Maximum number of unusual torsions for a passing molecule '
+                             '(default: %(default)s)')
+
+    parser.add_argument('-d', '--local-density',
+                        dest='local_density_threshold',
+                        type=float,
+                        default=10.0,
+                        metavar='<threshold>',
+                        help='Local density threshold for classifying a torsion as unusual '
+                             '(default: %(default)s)')
+
+    parser.add_argument('--incl-organometallics',
+                        dest='incl_organometallics',
+                        action='store_true',
+                        help='Include organometallic compounds in the search '
+                             '(default: organic compounds only)')
+
+    parser.add_argument('--generalisation',
+                        action='store_true',
+                        help='Turn on generalisation for searches')
+
+    parser.add_argument('--successfn',
+                        default='successes.mol',
+                        metavar='<file>',
+                        help='Output file for molecules that pass the filter '
+                             '(default: %(default)s)')
+
+    parser.add_argument('--failurefn',
+                        default='failures.mol',
+                        metavar='<file>',
+                        help='Output file for molecules that fail the filter '
+                             '(default: %(default)s)')
+
+    parser.add_argument('-u', '--unusual-torsions',
+                        dest='unusualtorsionsfn',
+                        default='unusual_torsions.csv',
+                        metavar='<file>',
+                        help='Output CSV file for unusual torsion details '
+                             '(default: %(default)s)')
+
+    return parser.parse_args()
+
+
+def create_mogul_engine(local_density_threshold, incl_organometallics, generalisation):
+    """Create and configure a geometry analyser engine.
+
+    Args:
+        local_density_threshold: Threshold for classifying torsions as unusual
+        incl_organometallics: Whether to include organometallic compounds
+        generalisation: Whether to enable generalisation for searches
+
+    Returns:
+        Configured ccdc.conformer.GeometryAnalyser instance
+    """
+    engine = conformer.GeometryAnalyser()
+
+    engine.settings.bond.analyse = False
+    engine.settings.angle.analyse = False
+    engine.settings.ring.analyse = False
+
+    engine.settings.torsion.local_density_threshold = local_density_threshold
+    engine.settings.generalisation = generalisation
+    engine.settings.organometallic_filter = 'all' if incl_organometallics else 'organics_only'
+
+    return engine
+
+
+def analysis(torsion_limit, input_filename, mode, engine, success_file, failure_file, unusual_torsion_file):
+    """Analyze molecules for unusual torsions and filter based on criteria.
+
+    Args:
+        torsion_limit: Maximum number of unusual torsions allowed
+        input_filename: Path to input molecule file
+        mode: 'absolute' or 'relative' filtering mode
+        engine: Configured GeometryAnalyser instance
+        success_file: Path to output file for passing molecules
+        failure_file: Path to output file for failing molecules
+        unusual_torsion_file: Path to CSV file for unusual torsion details
+    """
+    # Analyze all molecules and collect unusual torsion data
+    molecules = []
+    min_unusual_torsions = float('inf')
+
+    with io.MoleculeReader(input_filename) as mol_reader:
+        for molecule in mol_reader:
+            molecule.standardise_aromatic_bonds()
+            molecule.standardise_delocalised_bonds()
+
+            geometry_analysed_molecule = engine.analyse_molecule(molecule)
+
+            molecule.unusual_torsions = [
+                t for t in geometry_analysed_molecule.analysed_torsions
+                if t.unusual and t.enough_hits
+            ]
+            molecule.num_unusual_torsions = len(molecule.unusual_torsions)
+            molecules.append(molecule)
+
+            min_unusual_torsions = min(min_unusual_torsions, molecule.num_unusual_torsions)
+
+    # Write results
+    with io.MoleculeWriter(success_file) as passed_writer, \
+         io.MoleculeWriter(failure_file) as failed_writer, \
+         open(unusual_torsion_file, 'w', newline='') as csv_file:
+
+        csv_writer = csv.writer(csv_file)
+        csv_writer.writerow(['MoleculeIndex', 'Value', 'Zscore', 'LocalDensity', 'NumHits', 'Atoms'])
+
+        for idx, molecule in enumerate(molecules):
+            threshold = torsion_limit if mode == 'absolute' else min_unusual_torsions + torsion_limit
+            failed = molecule.num_unusual_torsions > threshold
+
+            if failed:
+                failed_writer.write(molecule)
+                for torsion in molecule.unusual_torsions:
+                    csv_writer.writerow([
+                        idx,
+                        torsion.value,
+                        torsion.z_score,
+                        torsion.local_density,
+                        torsion.nhits,
+                        ' '.join(torsion.atom_labels)
+                    ])
+            else:
+                passed_writer.write(molecule)
+
+
+def run():
+    """Main entry point for the script."""
+    args = parse_args()
+
+    if args.torsion_limit < 0:
+        raise ValueError('Torsion limit must be >= 0')
+
+    engine = create_mogul_engine(
+        args.local_density_threshold,
+        args.incl_organometallics,
+        args.generalisation
+    )
+
+    analysis(
+        args.torsion_limit,
+        args.inmolfn,
+        args.mode,
+        engine,
+        args.successfn,
+        args.failurefn,
+        args.unusualtorsionsfn,
+    )
+
+
+if __name__ == '__main__':
+    run()

scripts/filter_poses/ReadMe.md

@@ -0,0 +1,23 @@
+# Filter Poses
+
+This is a short script to filter molecular poses in a multi-molecule file based on the torsion probabilities. 
+Information will be printed to screen, or can be saved to a csv file.
+
+CCDC Python API Licence required, minimum version: 3.0.15
+
+Script can be run with any multimolecule file e.g. sdf.
+
+## Instructions on Running
+
+positional arguments:
+* input file; Input file (multi-molecule file).
+
+options:
+* -h, --help; Show this help message and exit.
+* -csv, --write-csv; Write a csv file for all the analysed conformers.
+
+Originally written by Jason Cole
+Updated by Chris Ringrose
+
+    For feedback or to report any issues please contact support@ccdc.cam.ac.uk
+